def test_system(command=None, options=None, exit_on_failure=False, output=False) :
binaries = {
'preprocess' : {
'*' : ['sff2fastq'],
'chimeras' : ['uchime'],
'denoise' : ['PyroDist', 'FCluster', 'PyroNoise'],
},
'cluster' : {
'*' : ['pagan'],
'labels' : ['blastn', 'makeblastdb']
},
'label' : {
'*' : ['blastn', 'makeblastdb']
},
'summary' : {},
'showcounts' : {},
'showlabels' : {},
'phylogeny' : {
'*' : ['pagan', 'exonerate', 'bppphysamp'],
'denovo' : ['raxml']
},
'heatmap' : {},
'wasabi' : {},
'test' : {}
}
def print_out(s) :
if output :
print s
else :
if 'not found' in s :
print >> stderr, s.lstrip()
fail = False
for b in [command] if command else binaries :
if binaries[b] :
print_out("checking system for %s command dependancies :" % bold(b))
for o in binaries[b] :
if o == '*' or not options or options[o] :
for p in binaries[b][o] :
installed = System.is_installed(p)
print_out(" %s %s%s" % (p, "" if o == "*" else "(needed for --%s) " % o,
bold_green("found.") if installed else bold_red("not found!")))
if not installed :
fail = True
print_out("")
# for some reason using pip to install cairo always fails
# so check for it here instead
# print "checking for python modules :"
# try :
# import cairo
# print " pycairo (needed by 'heatmap' command) " + bold_green("found.")
# except ImportError :
# print " pycairo (needed by 'heatmap' command) " + bold_red("not found!")
# fail = True
# print ""
if exit_on_failure and fail :
exit(1)
